Comments (3)
Once you have an HDF5-backed BSseq object (i.e. you've run HDF5Array::saveHDF5BackedSummarizedExperiment()
and you have the se.rds
and assays.h5
files) then you can load it back into R using HDF5Array::loadHDF5SummarizedExperiment()
.
There's no need for read.bismark()
once you're at this point, so I don't really understand what you're trying to do.
from bsseq.
this is good question! thanks @PeteHaitch for the response!
As a follow question -
if you subset a loaded bsseq
object in an R session backed by hdf5
do you need to manually resave on disk before using the modified bsseq
object for bsmooth()
?
here's an example after removing chromosomes Y and MT, where bsmooth()
doesn't seem to recognize the modified bsseq object. pls how can i resolve this? thanks!!!
chrMT_loci <- which(bismark_bsseq@rowRanges@seqnames == "MT")
chrY_loci <- which(bismark_bsseq@rowRanges@seqnames == "Y")
chr_loci_rm <- c(chrMT_loci, chrMT_loci)
bismark_bsseq <- bismark_bsseq[-chr_loci_rm,]
message("\n performing bsmoothing \n")
bismark_bsseq.fit <- BSmooth(BSseq = bismark_bsseq,
BPPARAM = MulticoreParam(workers = 24,progressbar = TRUE),
verbose = TRUE)
from bsseq.
if you subset a loaded bsseq object in an R session backed by hdf5 do you need to manually resave on disk before using the modified bsseq object for bsmooth()?
No, that shouldn't be necessary.
here's an example after removing chromosomes Y and MT, where bsmooth() doesn't seem to recognize the modified bsseq object. pls how can i resolve this?
I don't understand what you mean and the code you've pasted in doesn't show any output.
If you're having a problem please post a reproducible example so we can help you.
from bsseq.
Related Issues (20)
- read.bismark() too slow - input format issue? HOT 8
- BSmooth - Error in env[[as.character(i)]] <- value : wrong args for environment subassignment HOT 2
- Error: C stack usage 10847362 is too close to the limit HOT 3
- Is it possible to append metadata to the GRanges within BSseq objects? HOT 3
- Normalization of the WGBS smooth data HOT 5
- bsseq incompatible with tictoc library HOT 1
- Error BSmooth HOT 3
- read.bismark: option to change tmpdir in fread? HOT 4
- BSmooth with HDF5 realization backend error: Stop worker failed with the error: wrong args for environment subassignment HOT 5
- combineList: BACKEND Argument not working as intended HOT 1
- BSmooth.tstat issue HOT 11
- Updating beachmat to tatami HOT 1
- combine(sample1.smooth, sample2.smooth) gives in unsmooth results? HOT 4
- bsmooth() fails - Error in `h()`: ! error in evaluating the argument 'seed' in selecting a method for function 'DelayedArray': HDF5. File accessibility. Unable to open file. HOT 3
- error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark. HOT 26
- Represent a CpG with single row during import HOT 11
- exclude "Y" chromosome from bsseq object HOT 3
- Upcoming change to DelayedArray::realize() HOT 2
- No output from read.bismark with bismark cov.files HOT 14
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from bsseq.